@swarmdo/cli 1.4.8

package/dist/src/commands/init.js

@@ -0,0 +1,1116 @@
+/**
+ * V3 CLI Init Command
+ * Comprehensive initialization for Swarmdo with Claude Code integration
+ */
+import { output } from '../output.js';
+import { confirm, select, multiSelect, input } from '../prompt.js';
+import * as fs from 'fs';
+import * as path from 'path';
+import { executeInit, executeUpgrade, executeUpgradeWithMissing, DEFAULT_INIT_OPTIONS, MINIMAL_INIT_OPTIONS, FULL_INIT_OPTIONS, } from '../init/index.js';
+import { resolvePreset, presetNames } from '../init/presets.js';
+// Codex initialization action
+async function initCodexAction(ctx, options) {
+    const { force, minimal, full, dualMode } = options;
+    output.writeln();
+    output.writeln(output.bold('Initializing Swarmdo V3 for OpenAI Codex'));
+    output.writeln();
+    // Determine template
+    const template = minimal ? 'minimal' : full ? 'full' : 'default';
+    const spinner = output.createSpinner({ text: 'Initializing Codex project...' });
+    spinner.start();
+    try {
+        let CodexInitializer;
+        // Try multiple resolution strategies for the @swarmdo/codex package
+        // Use a variable to prevent TypeScript from statically resolving the optional module
+        const codexModuleId = '@swarmdo/codex';
+        const resolutionStrategies = [
+            // Strategy 1: Direct import (works if installed as CLI dependency)
+            async () => (await import(codexModuleId)).CodexInitializer,
+            // Strategy 2: Project node_modules (works if installed in user's project)
+            async () => {
+                const projectPath = path.join(ctx.cwd, 'node_modules', '@swarmdo', 'codex', 'dist', 'index.js');
+                if (fs.existsSync(projectPath)) {
+                    const mod = await import(`file://${projectPath}`);
+                    return mod.CodexInitializer;
+                }
+                throw new Error('Not found in project');
+            },
+            // Strategy 3: Global node_modules
+            async () => {
+                const { execSync } = await import('child_process');
+                const globalPath = execSync('npm root -g', { encoding: 'utf-8' }).trim();
+                const codexPath = path.join(globalPath, '@swarmdo', 'codex', 'dist', 'index.js');
+                if (fs.existsSync(codexPath)) {
+                    const mod = await import(`file://${codexPath}`);
+                    return mod.CodexInitializer;
+                }
+                throw new Error('Not found globally');
+            },
+        ];
+        for (const strategy of resolutionStrategies) {
+            try {
+                CodexInitializer = await strategy();
+                if (CodexInitializer)
+                    break;
+            }
+            catch {
+                // Try next strategy
+            }
+        }
+        if (!CodexInitializer) {
+            throw new Error('Cannot find module @swarmdo/codex');
+        }
+        const initializer = new CodexInitializer();
+        const result = await initializer.initialize({
+            projectPath: ctx.cwd,
+            template: template,
+            force,
+            dual: dualMode,
+        });
+        if (!result.success) {
+            spinner.fail('Codex initialization failed');
+            if (result.errors) {
+                for (const error of result.errors) {
+                    output.printError(error);
+                }
+            }
+            return { success: false, exitCode: 1 };
+        }
+        spinner.succeed('Codex project initialized successfully!');
+        output.writeln();
+        // Display summary
+        const summary = [];
+        summary.push(`Files: ${result.filesCreated.length} created`);
+        summary.push(`Skills: ${result.skillsGenerated.length} installed`);
+        output.printBox(summary.join('\n'), 'Summary');
+        output.writeln();
+        // Show what was created
+        output.printBox([
+            `AGENTS.md:     Main project instructions`,
+            `.agents/config.toml: Project configuration`,
+            `.agents/skills/: ${result.skillsGenerated.length} skills`,
+            `.codex/: Local overrides (gitignored)`,
+            dualMode ? `CLAUDE.md: Claude Code compatibility` : '',
+        ].filter(Boolean).join('\n'), 'OpenAI Codex Integration');
+        output.writeln();
+        // Warnings
+        if (result.warnings && result.warnings.length > 0) {
+            output.printWarning('Warnings:');
+            for (const warning of result.warnings.slice(0, 5)) {
+                output.printInfo(`  • ${warning}`);
+            }
+            if (result.warnings.length > 5) {
+                output.printInfo(`  ... and ${result.warnings.length - 5} more`);
+            }
+            output.writeln();
+        }
+        // Next steps
+        output.writeln(output.bold('Next steps:'));
+        output.printList([
+            `Review ${output.highlight('AGENTS.md')} for project instructions`,
+            `Add skills with ${output.highlight('$skill-name')} syntax`,
+            `Configure ${output.highlight('.agents/config.toml')} for your project`,
+            dualMode ? `Claude Code users can use ${output.highlight('CLAUDE.md')}` : '',
+        ].filter(Boolean));
+        return { success: true, data: result };
+    }
+    catch (error) {
+        spinner.fail('Codex initialization failed');
+        const errorMessage = error instanceof Error ? error.message : String(error);
+        // Handle module not found error gracefully
+        if (errorMessage.includes('Cannot find module') || errorMessage.includes('@swarmdo/codex')) {
+            output.printError('The @swarmdo/codex package is not installed.');
+            output.printInfo('Install it with: npm install @swarmdo/codex');
+            output.writeln();
+            output.printInfo('Alternatively, copy skills manually from .claude/skills/ to .agents/skills/');
+        }
+        else {
+            output.printError(`Failed to initialize: ${errorMessage}`);
+        }
+        return { success: false, exitCode: 1 };
+    }
+}
+// Check if project is already initialized with swarmdo.
+// #2207: .claude/settings.json alone is NOT a swarmdo marker — it's created by
+// Claude Code itself and exists in every Claude Code project. We require a
+// swarmdo-specific signal: either a claudeFlow section in settings.json, OR a
+// .mcp.json with a 'swarmdo' or 'swarmdo' server key, OR the swarmdo-only
+// .swarmdo/config.yaml. Using the bare file-existence check was causing
+// false-positives for new users whose only existing file was Claude Code's own
+// settings.json.
+function isInitialized(cwd) {
+    const claudeFlowPath = path.join(cwd, '.swarmdo', 'config.yaml');
+    const mcpJsonPath = path.join(cwd, '.mcp.json');
+    const settingsPath = path.join(cwd, '.claude', 'settings.json');
+    // Check .swarmdo/config.yaml — swarmdo-specific, always reliable
+    const hasClaudeFlow = fs.existsSync(claudeFlowPath);
+    // Check .claude/settings.json for swarmdo-specific content (claudeFlow section)
+    let hasSwarmdoSettings = false;
+    if (fs.existsSync(settingsPath)) {
+        try {
+            const parsed = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+            hasSwarmdoSettings =
+                parsed != null &&
+                    typeof parsed === 'object' &&
+                    'claudeFlow' in parsed;
+        }
+        catch { /* malformed — ignore */ }
+    }
+    // Check .mcp.json for swarmdo/swarmdo server key
+    let hasSwarmdoMcp = false;
+    if (fs.existsSync(mcpJsonPath)) {
+        try {
+            const parsed = JSON.parse(fs.readFileSync(mcpJsonPath, 'utf-8'));
+            hasSwarmdoMcp =
+                parsed != null &&
+                    typeof parsed === 'object' &&
+                    parsed.mcpServers != null &&
+                    typeof parsed.mcpServers === 'object' &&
+                    ('swarmdo' in parsed.mcpServers ||
+                        'swarmdo' in parsed.mcpServers);
+        }
+        catch { /* malformed — ignore */ }
+    }
+    return {
+        claude: hasSwarmdoSettings || hasSwarmdoMcp,
+        claudeFlow: hasClaudeFlow,
+    };
+}
+// Init subcommand (default)
+const initAction = async (ctx) => {
+    const force = ctx.flags.force;
+    const minimal = ctx.flags.minimal;
+    const full = ctx.flags.full;
+    const skipClaude = ctx.flags['skip-claude'];
+    const onlyClaude = ctx.flags['only-claude'];
+    // #2098A — the parser handles `--no-foo` by stripping the prefix and
+    // storing `flags.foo = false` (parser.ts:291-294), not by storing
+    // `flags['no-foo'] = true`. So `--no-global` lands as
+    // `ctx.flags.global === false`. The old read of `flags['no-global']`
+    // was always undefined and silently no-op'd — every user with the flag
+    // set still got `~/.claude/CLAUDE.md` modified. Read the real key.
+    const noGlobal = ctx.flags['no-global'] === true || ctx.flags['global'] === false;
+    const allAgents = ctx.flags['all-agents'];
+    const cloudMcp = ctx.flags['cloud-mcp'];
+    const codexMode = ctx.flags.codex;
+    const dualMode = ctx.flags.dual;
+    const cwd = ctx.cwd;
+    // If codex mode, use the Codex initializer
+    if (codexMode || dualMode) {
+        return initCodexAction(ctx, { codexMode, dualMode, force, minimal, full });
+    }
+    // Check if already initialized
+    const initialized = isInitialized(cwd);
+    const hasExisting = initialized.claude || initialized.claudeFlow;
+    if (hasExisting && !force) {
+        output.printWarning('Swarmdo appears to be already initialized');
+        if (initialized.claude)
+            output.printInfo('  Found: .claude/settings.json');
+        if (initialized.claudeFlow)
+            output.printInfo('  Found: .swarmdo/config.yaml');
+        output.printInfo('Use --force to reinitialize');
+        if (ctx.interactive) {
+            const proceed = await confirm({
+                message: 'Do you want to reinitialize? This will overwrite existing configuration.',
+                default: false,
+            });
+            if (!proceed) {
+                return { success: true, message: 'Initialization cancelled' };
+            }
+        }
+        else {
+            return { success: false, exitCode: 1, message: 'Already initialized' };
+        }
+    }
+    output.writeln();
+    output.writeln(output.bold('Initializing Swarmdo V3'));
+    output.writeln();
+    // Build init options based on flags
+    let options;
+    const presetFlag = ctx.flags.preset;
+    if (presetFlag) {
+        const p = resolvePreset(presetFlag);
+        if (!p) {
+            output.printError(`unknown preset '${presetFlag}' (choose: ${presetNames().join(', ')}; details: swarmdo preset list)`);
+            return { success: false, exitCode: 1 };
+        }
+        options = { ...p.options, targetDir: cwd, force };
+        output.printInfo(`Preset: ${p.title} — ${p.summary}`);
+    }
+    else if (minimal) {
+        options = { ...MINIMAL_INIT_OPTIONS, targetDir: cwd, force };
+    }
+    else if (full) {
+        options = { ...FULL_INIT_OPTIONS, targetDir: cwd, force };
+        // #2356: keep auth-gated cloud MCP servers opt-in even under --full. They
+        // require a login, get committed into .mcp.json, and add per-session MCP
+        // tool-definition token cost. --cloud-mcp restores the all-three behavior.
+        if (!cloudMcp) {
+            options.mcp = { ...options.mcp, swarmdoSwarm: false };
+        }
+    }
+    else {
+        options = { ...DEFAULT_INIT_OPTIONS, targetDir: cwd, force };
+    }
+    // Handle --skip-claude and --only-claude flags
+    if (skipClaude) {
+        options.components.settings = false;
+        options.components.skills = false;
+        options.components.commands = false;
+        options.components.agents = false;
+        options.components.helpers = false;
+        options.components.statusline = false;
+        options.components.mcp = false;
+        options.components.claudeMd = false;
+    }
+    if (onlyClaude) {
+        options.components.runtime = false;
+    }
+    // ADR-128 Phase 3 — restore full agent set (98 agents) when user explicitly
+    // requests it. Default is the ~24-agent substrate (core, consensus, swarm,
+    // sparc, testing). Pass --all-agents to get the old behavior.
+    if (allAgents) {
+        options.agents.all = true;
+    }
+    // #1744 — opt-out of the user-global ~/.claude/CLAUDE.md "Swarmdo Integration"
+    // pointer block. Default behavior (off) preserves current install for users
+    // who rely on it; opting in via --no-global keeps the global file pristine.
+    if (noGlobal) {
+        options.skipGlobalClaudeMd = true;
+    }
+    // Create spinner
+    const spinner = output.createSpinner({ text: 'Initializing...' });
+    spinner.start();
+    try {
+        // Execute initialization
+        const result = await executeInit(options);
+        if (!result.success) {
+            spinner.fail('Initialization failed');
+            for (const error of result.errors) {
+                output.printError(error);
+            }
+            return { success: false, exitCode: 1 };
+        }
+        spinner.succeed('Swarmdo V3 initialized successfully!');
+        output.writeln();
+        // Display summary
+        const summary = [];
+        if (result.created.directories.length > 0) {
+            summary.push(`Directories: ${result.created.directories.length} created`);
+        }
+        if (result.created.files.length > 0) {
+            summary.push(`Files: ${result.created.files.length} created`);
+        }
+        if (result.skipped.length > 0) {
+            summary.push(`Skipped: ${result.skipped.length} (already exist)`);
+        }
+        output.printBox(summary.join('\n'), 'Summary');
+        output.writeln();
+        // Show what was created
+        if (options.components.claudeMd || options.components.settings || options.components.skills || options.components.commands || options.components.agents) {
+            output.printBox([
+                options.components.claudeMd ? `CLAUDE.md:   Swarm guidance & configuration` : '',
+                options.components.settings ? `Settings:    .claude/settings.json` : '',
+                options.components.skills ? `Skills:      .claude/skills/ (${result.summary.skillsCount} skills)` : '',
+                options.components.commands ? `Commands:    .claude/commands/sDo/ (${result.summary.commandsCount} commands)` : '',
+                options.components.agents ? `Agents:      .claude/agents/ (${result.summary.agentsCount} agents)` : '',
+                options.components.helpers ? `Helpers:     .claude/helpers/` : '',
+                options.components.mcp ? `MCP:         .mcp.json` : '',
+            ].filter(Boolean).join('\n'), 'Claude Code Integration');
+            output.writeln();
+        }
+        if (options.components.runtime) {
+            output.printBox([
+                `Config:      .swarmdo/config.yaml`,
+                `Data:        .swarmdo/data/`,
+                `Logs:        .swarmdo/logs/`,
+                `Sessions:    .swarmdo/sessions/`,
+            ].join('\n'), 'V3 Runtime');
+            output.writeln();
+        }
+        // Hooks summary
+        if (result.summary.hooksEnabled > 0) {
+            output.printInfo(`Hooks: ${result.summary.hooksEnabled} hook types enabled in settings.json`);
+            output.writeln();
+        }
+        // Handle --start-all or --start-daemon
+        const startAll = ctx.flags['start-all'] || ctx.flags.startAll;
+        const startDaemon = ctx.flags['start-daemon'] || ctx.flags.startDaemon || startAll;
+        if (startDaemon || startAll) {
+            output.writeln();
+            output.printInfo('Starting services...');
+            const { execSync } = await import('child_process');
+            // Initialize memory database
+            if (startAll) {
+                try {
+                    output.writeln(output.dim('  Initializing memory database...'));
+                    execSync('npx @swarmdo/cli@latest memory init 2>/dev/null', {
+                        stdio: 'pipe',
+                        cwd: ctx.cwd,
+                        timeout: 30000
+                    });
+                    output.writeln(output.success('  ✓ Memory initialized'));
+                }
+                catch {
+                    output.writeln(output.dim('  Memory database already exists'));
+                }
+            }
+            // Start daemon — #2407 fix
+            //
+            // The previous version used `daemon start ... &` (shell background)
+            // which made execSync return as soon as the shell forked, BEFORE the
+            // daemon process wrote its PID file. Concurrent init runs
+            // (devcontainer setup + VS Code task + MCP hook firing within ~500 ms)
+            // all saw an empty PID file via getBackgroundDaemonPid(), so
+            // daemon.ts:99-103's dedup short-circuit didn't fire — every caller
+            // spawned its own daemon. One incident accumulated 39 zombie daemons
+            // holding ~8.5 GiB resident, which together with macOS compressor
+            // pressure (27 GiB compressed) caused the configd watchdog timeout
+            // and the 2026-06-15 21:06 kernel panic.
+            //
+            // Fix: drop the shell `&`. `daemon start` (default non-foreground
+            // mode) already forks its own detached background process via
+            // startBackgroundDaemon() AND writes the PID file BEFORE returning,
+            // so execSync without `&` waits for the dedup-relevant PID-file
+            // write but does NOT wait for the daemon itself to exit. Timeout
+            // bumped to 30s for npx cold-cache scenarios.
+            if (startDaemon) {
+                try {
+                    output.writeln(output.dim('  Starting daemon...'));
+                    execSync('npx @swarmdo/cli@latest daemon start 2>/dev/null', {
+                        stdio: 'pipe',
+                        cwd: ctx.cwd,
+                        timeout: 30000
+                    });
+                    output.writeln(output.success('  ✓ Daemon started'));
+                }
+                catch {
+                    // Daemon dedup hit (already running) OR spawn timed out.
+                    // Either way the worst case is a single retry on next init,
+                    // not a forked race producing N zombies.
+                    output.writeln(output.warning('  Daemon may already be running'));
+                }
+            }
+            // Initialize swarm
+            if (startAll) {
+                try {
+                    output.writeln(output.dim('  Initializing swarm...'));
+                    execSync('npx @swarmdo/cli@latest swarm init --topology hierarchical 2>/dev/null', {
+                        stdio: 'pipe',
+                        cwd: ctx.cwd,
+                        timeout: 30000
+                    });
+                    output.writeln(output.success('  ✓ Swarm initialized'));
+                }
+                catch {
+                    output.writeln(output.dim('  Swarm initialization skipped'));
+                }
+            }
+            output.writeln();
+            output.printSuccess('All services started');
+        }
+        // Handle --with-embeddings
+        const withEmbeddings = ctx.flags['with-embeddings'] || ctx.flags.withEmbeddings;
+        const embeddingModel = (ctx.flags['embedding-model'] || ctx.flags.embeddingModel || 'Xenova/all-MiniLM-L6-v2');
+        if (withEmbeddings) {
+            output.writeln();
+            output.printInfo('Initializing ONNX embedding subsystem...');
+            const { execFileSync: execFileInit } = await import('child_process');
+            // Validate embeddingModel: must match pattern org/model-name (CRIT-02)
+            if (!/^[a-zA-Z0-9_-]+\/[a-zA-Z0-9._-]+$/.test(embeddingModel)) {
+                throw new Error(`Invalid embedding model name: ${embeddingModel}`);
+            }
+            try {
+                output.writeln(output.dim(`  Model: ${embeddingModel}`));
+                output.writeln(output.dim('  Hyperbolic: Enabled (Poincaré ball)'));
+                execFileInit('npx', [
+                    '@swarmdo/cli@latest', 'embeddings', 'init',
+                    '--model', embeddingModel,
+                    '--no-download', '--force',
+                ], {
+                    stdio: 'pipe',
+                    cwd: ctx.cwd,
+                    timeout: 30000,
+                });
+                output.writeln(output.success('  ✓ Embeddings initialized'));
+                output.writeln(output.dim('    Run "embeddings init --download" to download model'));
+            }
+            catch (err) {
+                output.writeln(output.warning('  Embedding initialization skipped (run manually)'));
+            }
+        }
+        if (!startDaemon && !startAll) {
+            const bin = (process.argv[1] || '').includes('swarmdo') ? 'swarmdo' : 'swarmdo';
+            output.writeln(output.bold('Next steps:'));
+            output.printList([
+                `Run ${output.highlight(`${bin} daemon start`)} to start background workers`,
+                `Run ${output.highlight(`${bin} memory init`)} to initialize memory database`,
+                `Run ${output.highlight(`${bin} swarm init`)} to initialize a swarm`,
+                `Or use ${output.highlight(`${bin} init --start-all`)} to do all of the above`,
+                options.components.settings ? `Review ${output.highlight('.claude/settings.json')} for hook configurations` : '',
+                // ADR-150 — surface the new metaharness scorecard to every new user.
+                // Optional dep; the command degrades gracefully when not installed.
+                `Run ${output.highlight(`${bin} metaharness score`)} for a 5-dim harness readiness scorecard (ADR-150)`,
+            ].filter(Boolean));
+        }
+        if (ctx.flags.format === 'json') {
+            output.printJson(result);
+        }
+        return { success: true, data: result };
+    }
+    catch (error) {
+        spinner.fail('Initialization failed');
+        output.printError(`Failed to initialize: ${error instanceof Error ? error.message : String(error)}`);
+        return { success: false, exitCode: 1 };
+    }
+};
+// Wizard subcommand for interactive setup
+const wizardCommand = {
+    name: 'wizard',
+    description: 'Interactive setup wizard for comprehensive configuration',
+    action: async (ctx) => {
+        output.writeln();
+        output.writeln(output.bold('Swarmdo V3 Setup Wizard'));
+        output.writeln(output.dim('Answer questions to configure your project'));
+        output.writeln();
+        try {
+            // Start with base options
+            const options = { ...DEFAULT_INIT_OPTIONS, targetDir: ctx.cwd };
+            // Configuration preset
+            const preset = await select({
+                message: 'Select configuration preset:',
+                options: [
+                    { value: 'default', label: 'Default', hint: 'Recommended settings for most projects' },
+                    { value: 'minimal', label: 'Minimal', hint: 'Core features only' },
+                    { value: 'full', label: 'Full', hint: 'All features enabled' },
+                    { value: 'custom', label: 'Custom', hint: 'Choose each component' },
+                ],
+            });
+            if (preset === 'minimal') {
+                Object.assign(options, MINIMAL_INIT_OPTIONS);
+                options.targetDir = ctx.cwd;
+            }
+            else if (preset === 'full') {
+                Object.assign(options, FULL_INIT_OPTIONS);
+                options.targetDir = ctx.cwd;
+            }
+            else if (preset === 'custom') {
+                // Component selection
+                const components = await multiSelect({
+                    message: 'Select components to initialize:',
+                    options: [
+                        { value: 'claudeMd', label: 'CLAUDE.md', hint: 'Swarm guidance and project configuration', selected: true },
+                        { value: 'settings', label: 'settings.json', hint: 'Claude Code hooks configuration', selected: true },
+                        { value: 'skills', label: 'Skills', hint: 'Claude Code skills in .claude/skills/', selected: true },
+                        { value: 'commands', label: 'Commands', hint: 'Claude Code commands in .claude/commands/', selected: true },
+                        { value: 'agents', label: 'Agents', hint: 'Agent definitions in .claude/agents/', selected: true },
+                        { value: 'helpers', label: 'Helpers', hint: 'Utility scripts in .claude/helpers/', selected: true },
+                        { value: 'statusline', label: 'Statusline', hint: 'Shell statusline integration', selected: false },
+                        { value: 'mcp', label: 'MCP', hint: '.mcp.json for MCP server configuration', selected: true },
+                        { value: 'runtime', label: 'Runtime', hint: '.swarmdo/ directory for V3 runtime', selected: true },
+                    ],
+                });
+                options.components.claudeMd = components.includes('claudeMd');
+                options.components.settings = components.includes('settings');
+                options.components.skills = components.includes('skills');
+                options.components.commands = components.includes('commands');
+                options.components.agents = components.includes('agents');
+                options.components.helpers = components.includes('helpers');
+                options.components.statusline = components.includes('statusline');
+                options.components.mcp = components.includes('mcp');
+                options.components.runtime = components.includes('runtime');
+                // Skills selection
+                if (options.components.skills) {
+                    const skillSets = await multiSelect({
+                        message: 'Select skill sets:',
+                        options: [
+                            { value: 'core', label: 'Core', hint: 'Swarm, memory, SPARC skills', selected: true },
+                            { value: 'agentdb', label: 'AgentDB', hint: 'Vector database skills', selected: true },
+                            { value: 'github', label: 'GitHub', hint: 'GitHub integration skills', selected: true },
+                            { value: 'v3', label: 'V3', hint: 'V3 implementation skills', selected: true },
+                            { value: 'efficiency', label: 'Efficiency', hint: 'caveman-compress + ponytail (token savings, YAGNI)', selected: true },
+                        ],
+                    });
+                    options.skills.core = skillSets.includes('core');
+                    options.skills.agentdb = skillSets.includes('agentdb');
+                    options.skills.github = skillSets.includes('github');
+                    options.skills.v3 = skillSets.includes('v3');
+                    options.skills.efficiency = skillSets.includes('efficiency');
+                }
+                // Hooks selection
+                if (options.components.settings) {
+                    const hooks = await multiSelect({
+                        message: 'Select hooks to enable:',
+                        options: [
+                            { value: 'preToolUse', label: 'PreToolUse', hint: 'Before tool execution', selected: true },
+                            { value: 'postToolUse', label: 'PostToolUse', hint: 'After tool execution', selected: true },
+                            { value: 'userPromptSubmit', label: 'UserPromptSubmit', hint: 'Task routing', selected: true },
+                            { value: 'sessionStart', label: 'SessionStart', hint: 'Session initialization', selected: true },
+                            { value: 'stop', label: 'Stop', hint: 'Task completion evaluation', selected: true },
+                            { value: 'notification', label: 'Notification', hint: 'Swarm notifications', selected: true },
+                            { value: 'permissionRequest', label: 'PermissionRequest', hint: 'Auto-allow swarmdo tools', selected: true },
+                        ],
+                    });
+                    options.hooks.preToolUse = hooks.includes('preToolUse');
+                    options.hooks.postToolUse = hooks.includes('postToolUse');
+                    options.hooks.userPromptSubmit = hooks.includes('userPromptSubmit');
+                    options.hooks.sessionStart = hooks.includes('sessionStart');
+                    options.hooks.stop = hooks.includes('stop');
+                    options.hooks.notification = hooks.includes('notification');
+                }
+            }
+            // Swarm topology (for all presets)
+            const topology = await select({
+                message: 'Select swarm topology:',
+                options: [
+                    { value: 'hierarchical-mesh', label: 'Hierarchical Mesh', hint: 'Best for complex projects (recommended)' },
+                    { value: 'mesh', label: 'Mesh', hint: 'Peer-to-peer coordination' },
+                    { value: 'hierarchical', label: 'Hierarchical', hint: 'Tree-based coordination' },
+                    { value: 'adaptive', label: 'Adaptive', hint: 'Dynamic topology switching' },
+                ],
+            });
+            options.runtime.topology = topology;
+            // Max agents
+            const maxAgents = await input({
+                message: 'Maximum concurrent agents:',
+                default: String(options.runtime.maxAgents),
+                validate: (v) => {
+                    const n = parseInt(v);
+                    return (!isNaN(n) && n > 0 && n <= 50) || 'Enter a number between 1 and 50';
+                },
+            });
+            options.runtime.maxAgents = parseInt(maxAgents);
+            // Memory backend
+            const memoryBackend = await select({
+                message: 'Select memory backend:',
+                options: [
+                    { value: 'hybrid', label: 'Hybrid', hint: 'SQLite + AgentDB (recommended)' },
+                    { value: 'agentdb', label: 'AgentDB', hint: '150x faster vector search' },
+                    { value: 'sqlite', label: 'SQLite', hint: 'Standard SQL storage' },
+                    { value: 'memory', label: 'In-Memory', hint: 'Fast but non-persistent' },
+                ],
+            });
+            options.runtime.memoryBackend = memoryBackend;
+            // HNSW indexing
+            if (memoryBackend === 'agentdb' || memoryBackend === 'hybrid') {
+                const enableHNSW = await confirm({
+                    message: 'Enable HNSW indexing for faster vector search?',
+                    default: true,
+                });
+                options.runtime.enableHNSW = enableHNSW;
+            }
+            // Neural learning
+            const enableNeural = await confirm({
+                message: 'Enable neural pattern learning?',
+                default: options.runtime.enableNeural,
+            });
+            options.runtime.enableNeural = enableNeural;
+            // ADR-049: Self-Learning Memory capabilities
+            if (memoryBackend === 'agentdb' || memoryBackend === 'hybrid') {
+                const enableSelfLearning = await confirm({
+                    message: 'Enable self-learning memory? (LearningBridge + Knowledge Graph + Agent Scopes)',
+                    default: true,
+                });
+                options.runtime.enableLearningBridge = enableSelfLearning && enableNeural;
+                options.runtime.enableMemoryGraph = enableSelfLearning;
+                options.runtime.enableAgentScopes = enableSelfLearning;
+            }
+            else {
+                options.runtime.enableLearningBridge = false;
+                options.runtime.enableMemoryGraph = false;
+                options.runtime.enableAgentScopes = false;
+            }
+            // Embeddings configuration
+            const enableEmbeddings = await confirm({
+                message: 'Enable ONNX embedding system with hyperbolic support?',
+                default: true,
+            });
+            let embeddingModel = 'Xenova/all-MiniLM-L6-v2';
+            if (enableEmbeddings) {
+                embeddingModel = await select({
+                    message: 'Select embedding model:',
+                    options: [
+                        { value: 'Xenova/all-MiniLM-L6-v2', label: 'MiniLM L6 (384d)', hint: 'Fast, good quality (recommended)' },
+                        { value: 'Xenova/all-mpnet-base-v2', label: 'MPNet Base (768d)', hint: 'Higher quality, more memory' },
+                    ],
+                });
+            }
+            // Execute initialization
+            output.writeln();
+            const spinner = output.createSpinner({ text: 'Initializing...' });
+            spinner.start();
+            const result = await executeInit(options);
+            if (!result.success) {
+                spinner.fail('Initialization failed');
+                for (const error of result.errors) {
+                    output.printError(error);
+                }
+                return { success: false, exitCode: 1 };
+            }
+            spinner.succeed('Setup complete!');
+            // Initialize embeddings if enabled
+            let embeddingsInitialized = false;
+            if (enableEmbeddings) {
+                output.writeln();
+                output.printInfo('Initializing ONNX embedding subsystem...');
+                const { execFileSync } = await import('child_process');
+                // Validate embeddingModel: must match pattern org/model-name (CRIT-02)
+                if (!/^[a-zA-Z0-9_-]+\/[a-zA-Z0-9._-]+$/.test(embeddingModel)) {
+                    throw new Error(`Invalid embedding model name: ${embeddingModel}`);
+                }
+                try {
+                    execFileSync('npx', [
+                        '@swarmdo/cli@latest', 'embeddings', 'init',
+                        '--model', embeddingModel,
+                        '--no-download', '--force',
+                    ], {
+                        stdio: 'pipe',
+                        cwd: ctx.cwd,
+                        timeout: 30000,
+                    });
+                    output.writeln(output.success('  ✓ Embeddings configured'));
+                    embeddingsInitialized = true;
+                }
+                catch {
+                    output.writeln(output.dim('  Embeddings will be configured on first use'));
+                }
+            }
+            output.writeln();
+            // Summary table
+            output.printTable({
+                columns: [
+                    { key: 'setting', header: 'Setting', width: 20 },
+                    { key: 'value', header: 'Value', width: 40 },
+                ],
+                data: [
+                    { setting: 'Preset', value: preset },
+                    { setting: 'Topology', value: options.runtime.topology },
+                    { setting: 'Max Agents', value: String(options.runtime.maxAgents) },
+                    { setting: 'Memory Backend', value: options.runtime.memoryBackend },
+                    { setting: 'HNSW Indexing', value: options.runtime.enableHNSW ? 'Enabled' : 'Disabled' },
+                    { setting: 'Neural Learning', value: options.runtime.enableNeural ? 'Enabled' : 'Disabled' },
+                    { setting: 'Self-Learning', value: options.runtime.enableLearningBridge ? 'LearningBridge + Graph + Scopes' : 'Disabled' },
+                    { setting: 'Embeddings', value: enableEmbeddings ? `${embeddingModel} (hyperbolic)` : 'Disabled' },
+                    { setting: 'Skills', value: `${result.summary.skillsCount} installed` },
+                    { setting: 'Commands', value: `${result.summary.commandsCount} installed` },
+                    { setting: 'Agents', value: `${result.summary.agentsCount} installed` },
+                    { setting: 'Hooks', value: `${result.summary.hooksEnabled} enabled` },
+                ],
+            });
+            return { success: true, data: result };
+        }
+        catch (error) {
+            if (error instanceof Error && error.message === 'User cancelled') {
+                output.printInfo('Setup cancelled');
+                return { success: true };
+            }
+            throw error;
+        }
+    },
+};
+// Check subcommand
+const checkCommand = {
+    name: 'check',
+    description: 'Check if Swarmdo is initialized',
+    action: async (ctx) => {
+        const initialized = isInitialized(ctx.cwd);
+        const result = {
+            initialized: initialized.claude || initialized.claudeFlow,
+            claude: initialized.claude,
+            claudeFlow: initialized.claudeFlow,
+            paths: {
+                claudeSettings: initialized.claude ? path.join(ctx.cwd, '.claude', 'settings.json') : null,
+                claudeFlowConfig: initialized.claudeFlow ? path.join(ctx.cwd, '.swarmdo', 'config.yaml') : null,
+            },
+        };
+        if (ctx.flags.format === 'json') {
+            output.printJson(result);
+            return { success: true, data: result };
+        }
+        if (result.initialized) {
+            output.printSuccess('Swarmdo is initialized');
+            if (initialized.claude) {
+                output.printInfo(`  Claude Code: .claude/settings.json`);
+            }
+            if (initialized.claudeFlow) {
+                output.printInfo(`  V3 Runtime: .swarmdo/config.yaml`);
+            }
+        }
+        else {
+            output.printWarning('Swarmdo is not initialized in this directory');
+            output.printInfo('Run "swarmdo init" to initialize');
+        }
+        return { success: true, data: result };
+    },
+};
+// Skills subcommand
+const skillsCommand = {
+    name: 'skills',
+    description: 'Initialize only skills',
+    options: [
+        { name: 'all', description: 'Install all skills', type: 'boolean', default: false },
+        { name: 'core', description: 'Install core skills', type: 'boolean', default: true },
+        { name: 'agentdb', description: 'Install AgentDB skills', type: 'boolean', default: false },
+        { name: 'github', description: 'Install GitHub skills', type: 'boolean', default: false },
+        { name: 'v3', description: 'Install V3 skills', type: 'boolean', default: false },
+    ],
+    action: async (ctx) => {
+        const options = {
+            ...MINIMAL_INIT_OPTIONS,
+            targetDir: ctx.cwd,
+            force: ctx.flags.force,
+            components: {
+                settings: false,
+                skills: true,
+                commands: false,
+                agents: false,
+                helpers: false,
+                statusline: false,
+                mcp: false,
+                runtime: false,
+                claudeMd: false,
+            },
+            skills: {
+                all: ctx.flags.all,
+                core: ctx.flags.core,
+                efficiency: ctx.flags.core || ctx.flags.all,
+                agentdb: ctx.flags.agentdb,
+                github: ctx.flags.github,
+                browser: false,
+                v3: ctx.flags.v3,
+                dualMode: false,
+            },
+        };
+        const spinner = output.createSpinner({ text: 'Installing skills...' });
+        spinner.start();
+        const result = await executeInit(options);
+        if (result.success) {
+            spinner.succeed(`Installed ${result.summary.skillsCount} skills`);
+        }
+        else {
+            spinner.fail('Failed to install skills');
+            for (const error of result.errors) {
+                output.printError(error);
+            }
+        }
+        return { success: result.success, data: result };
+    },
+};
+// Hooks subcommand
+const hooksCommand = {
+    name: 'hooks',
+    description: 'Initialize only hooks configuration',
+    options: [
+        { name: 'all', description: 'Enable all hooks', type: 'boolean', default: true },
+        { name: 'minimal', description: 'Enable only essential hooks', type: 'boolean', default: false },
+    ],
+    action: async (ctx) => {
+        const minimal = ctx.flags.minimal;
+        const options = {
+            ...DEFAULT_INIT_OPTIONS,
+            targetDir: ctx.cwd,
+            force: ctx.flags.force,
+            components: {
+                settings: true,
+                skills: false,
+                commands: false,
+                agents: false,
+                // #2350: helpers MUST ship with the hooks subcommand. The hook entries
+                // in settings.json point at `.claude/helpers/hook-handler.cjs`; if
+                // that file doesn't exist, settings-generator (#1744 fix) drops the
+                // hooks block entirely — so the one subcommand whose stated purpose
+                // is "Initialize only hooks configuration" produced settings.json
+                // with no `hooks` key while reporting "N hooks enabled".
+                helpers: true,
+                statusline: false,
+                mcp: false,
+                runtime: false,
+                claudeMd: false,
+            },
+            hooks: minimal
+                ? {
+                    preToolUse: true,
+                    postToolUse: true,
+                    userPromptSubmit: false,
+                    sessionStart: false,
+                    stop: false,
+                    preCompact: false,
+                    notification: false,
+                    teammateIdle: false,
+                    taskCompleted: false,
+                    timeout: 5000,
+                    continueOnError: true,
+                }
+                : DEFAULT_INIT_OPTIONS.hooks,
+        };
+        const spinner = output.createSpinner({ text: 'Creating hooks configuration...' });
+        spinner.start();
+        const result = await executeInit(options);
+        if (result.success) {
+            spinner.succeed(`Created settings.json with ${result.summary.hooksEnabled} hooks enabled`);
+        }
+        else {
+            spinner.fail('Failed to create hooks configuration');
+            for (const error of result.errors) {
+                output.printError(error);
+            }
+        }
+        return { success: result.success, data: result };
+    },
+};
+// Upgrade subcommand - updates helpers without losing user data
+const upgradeCommand = {
+    name: 'upgrade',
+    description: 'Update statusline and helpers while preserving existing data',
+    options: [
+        {
+            name: 'verbose',
+            short: 'v',
+            description: 'Show detailed output',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'add-missing',
+            short: 'a',
+            description: 'Add any new skills, agents, and commands that are missing',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'settings',
+            short: 's',
+            description: 'Merge new settings (Agent Teams, hooks) into existing settings.json',
+            type: 'boolean',
+            default: false,
+        },
+    ],
+    action: async (ctx) => {
+        const addMissing = (ctx.flags['add-missing'] || ctx.flags.addMissing);
+        const upgradeSettings = (ctx.flags.settings);
+        output.writeln();
+        output.writeln(output.bold('Upgrading Swarmdo'));
+        if (addMissing && upgradeSettings) {
+            output.writeln(output.dim('Updates helpers, settings, and adds any missing skills/agents/commands'));
+        }
+        else if (addMissing) {
+            output.writeln(output.dim('Updates helpers and adds any missing skills/agents/commands'));
+        }
+        else if (upgradeSettings) {
+            output.writeln(output.dim('Updates helpers and merges new settings (Agent Teams, hooks)'));
+        }
+        else {
+            output.writeln(output.dim('Updates helpers while preserving your existing data'));
+        }
+        output.writeln();
+        const spinnerText = upgradeSettings
+            ? 'Upgrading helpers and settings...'
+            : (addMissing ? 'Upgrading and adding missing assets...' : 'Upgrading...');
+        const spinner = output.createSpinner({ text: spinnerText });
+        spinner.start();
+        try {
+            const result = addMissing
+                ? await executeUpgradeWithMissing(ctx.cwd, upgradeSettings)
+                : await executeUpgrade(ctx.cwd, upgradeSettings);
+            if (!result.success) {
+                spinner.fail('Upgrade failed');
+                for (const error of result.errors) {
+                    output.printError(error);
+                }
+                return { success: false, exitCode: 1 };
+            }
+            spinner.succeed('Upgrade complete!');
+            output.writeln();
+            // Show what was updated
+            if (result.updated.length > 0) {
+                output.printBox(result.updated.map(f => `✓ ${f}`).join('\n'), 'Updated (latest version)');
+                output.writeln();
+            }
+            // Show what was created
+            if (result.created.length > 0) {
+                output.printBox(result.created.map(f => `+ ${f}`).join('\n'), 'Created (new files)');
+                output.writeln();
+            }
+            // Show what was preserved
+            if (result.preserved.length > 0 && ctx.flags.verbose) {
+                output.printBox(result.preserved.map(f => `• ${f}`).join('\n'), 'Preserved (existing data kept)');
+                output.writeln();
+            }
+            else if (result.preserved.length > 0) {
+                output.printInfo(`Preserved ${result.preserved.length} existing data files`);
+                output.writeln();
+            }
+            // Show added assets (when --add-missing flag is used)
+            if (result.addedSkills && result.addedSkills.length > 0) {
+                output.printBox(result.addedSkills.map(s => `+ ${s}`).join('\n'), `Added Skills (${result.addedSkills.length} new)`);
+                output.writeln();
+            }
+            if (result.addedAgents && result.addedAgents.length > 0) {
+                output.printBox(result.addedAgents.map(a => `+ ${a}`).join('\n'), `Added Agents (${result.addedAgents.length} new)`);
+                output.writeln();
+            }
+            if (result.addedCommands && result.addedCommands.length > 0) {
+                output.printBox(result.addedCommands.map(c => `+ ${c}`).join('\n'), `Added Commands (${result.addedCommands.length} new)`);
+                output.writeln();
+            }
+            // Show settings updates
+            if (result.settingsUpdated && result.settingsUpdated.length > 0) {
+                output.printBox(result.settingsUpdated.map(s => `+ ${s}`).join('\n'), 'Settings Updated');
+                output.writeln();
+            }
+            output.printSuccess('Your statusline helper has been updated to the latest version');
+            output.printInfo('Existing metrics and learning data were preserved');
+            // Show settings summary
+            if (upgradeSettings && result.settingsUpdated && result.settingsUpdated.length > 0) {
+                output.printSuccess('Settings.json updated with new Agent Teams configuration');
+            }
+            // Show summary for --add-missing
+            if (addMissing) {
+                const totalAdded = (result.addedSkills?.length || 0) + (result.addedAgents?.length || 0) + (result.addedCommands?.length || 0);
+                if (totalAdded > 0) {
+                    output.printSuccess(`Added ${totalAdded} missing assets to your project`);
+                }
+                else {
+                    output.printInfo('All skills, agents, and commands are already up to date');
+                }
+            }
+            if (ctx.flags.format === 'json') {
+                output.printJson(result);
+            }
+            return { success: true, data: result };
+        }
+        catch (error) {
+            spinner.fail('Upgrade failed');
+            output.printError(`Failed to upgrade: ${error instanceof Error ? error.message : String(error)}`);
+            return { success: false, exitCode: 1 };
+        }
+    },
+};
+// Main init command
+export const initCommand = {
+    name: 'init',
+    description: 'Initialize Swarmdo in the current directory',
+    subcommands: [wizardCommand, checkCommand, skillsCommand, hooksCommand, upgradeCommand],
+    options: [
+        {
+            name: 'force',
+            short: 'f',
+            description: 'Overwrite existing configuration',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'minimal',
+            short: 'm',
+            description: 'Create minimal configuration',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'full',
+            description: 'Create full configuration with all components',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'preset',
+            description: 'Apply a named configuration tier: minimal|basic|standard|advanced|max (see: swarmdo preset list)',
+            type: 'string',
+        },
+        {
+            // #2356: under --full, the auth-gated cloud MCP servers (swarmdo-swarm,
+            // tool-definition token cost every session. Keep them opt-in even with
+            // --full; pass --cloud-mcp to register them.
+            name: 'cloud-mcp',
+            description: 'Register auth-gated cloud MCP servers (swarmdo-swarm) in .mcp.json (only relevant with --full)',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'skip-claude',
+            description: 'Skip .claude/ directory creation (runtime only)',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'only-claude',
+            description: 'Only create .claude/ directory (skip runtime)',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'no-global',
+            description: 'Skip the ~/.claude/CLAUDE.md "Swarmdo Integration" pointer block (#1744)',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'start-all',
+            description: 'Auto-start daemon, memory, and swarm after init',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'start-daemon',
+            description: 'Auto-start daemon after init',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'with-embeddings',
+            description: 'Initialize ONNX embedding subsystem with hyperbolic support',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'embedding-model',
+            description: 'ONNX embedding model to use',
+            type: 'string',
+            default: 'Xenova/all-MiniLM-L6-v2',
+            choices: ['Xenova/all-MiniLM-L6-v2', 'Xenova/all-mpnet-base-v2'],
+        },
+        {
+            name: 'codex',
+            description: 'Initialize for OpenAI Codex CLI (creates AGENTS.md, .agents/)',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'dual',
+            description: 'Initialize for both Claude Code and OpenAI Codex',
+            type: 'boolean',
+            default: false,
+        },
+        {
+            name: 'all-agents',
+            description: 'Install all agent categories (ADR-128: default is ~24 substrate agents; this restores the full set of ~89)',
+            type: 'boolean',
+            default: false,
+        },
+    ],
+    examples: [
+        { command: 'swarmdo init', description: 'Initialize with default configuration' },
+        { command: 'swarmdo init --start-all', description: 'Initialize and start daemon, memory, swarm' },
+        { command: 'swarmdo init --start-daemon', description: 'Initialize and start daemon only' },
+        { command: 'swarmdo init --minimal', description: 'Initialize with minimal configuration' },
+        { command: 'swarmdo init --full', description: 'Initialize with all components' },
+        { command: 'swarmdo init --force', description: 'Reinitialize and overwrite existing config' },
+        { command: 'swarmdo init --only-claude', description: 'Only create Claude Code integration' },
+        { command: 'swarmdo init --skip-claude', description: 'Only create V3 runtime' },
+        { command: 'swarmdo init wizard', description: 'Interactive setup wizard' },
+        { command: 'swarmdo init --with-embeddings', description: 'Initialize with ONNX embeddings' },
+        { command: 'swarmdo init --with-embeddings --embedding-model Xenova/all-mpnet-base-v2', description: 'Use larger embedding model' },
+        { command: 'swarmdo init skills --all', description: 'Install all available skills' },
+        { command: 'swarmdo init hooks --minimal', description: 'Create minimal hooks configuration' },
+        { command: 'swarmdo init upgrade', description: 'Update helpers while preserving data' },
+        { command: 'swarmdo init upgrade --settings', description: 'Update helpers and merge new settings (Agent Teams)' },
+        { command: 'swarmdo init upgrade --verbose', description: 'Show detailed upgrade info' },
+        { command: 'swarmdo init --codex', description: 'Initialize for OpenAI Codex (AGENTS.md)' },
+        { command: 'swarmdo init --codex --full', description: 'Codex init with all 137+ skills' },
+        { command: 'swarmdo init --dual', description: 'Initialize for both Claude Code and Codex' },
+        { command: 'swarmdo init --all-agents', description: 'Install all agent categories (~89 agents; ADR-128 opt-in)' },
+    ],
+    action: initAction,
+};
+export default initCommand;
+//# sourceMappingURL=init.js.map